Disease Clusters?

Groups of diseases that share a large number of curated genes with each other, computed via label propagation over the shared-gene similarity graph. See also Shared-Gene Disease Pairs for pairwise comparisons.

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Cluster 54

15 diseases · 20 shared-gene connections
15 Diseases
189 Unique genes
0.091 Avg. similarity score
Microcephaly Most-connected disease (9 links)
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Disease Searched: Microcephaly, postnatal progressive, with seizures and brain atrophy Pinned (dragged)
Node size = connections within this cluster · edge thickness = similarity strength · hover an edge for its details · click a node to select it and show its pairs below (double-click or Ctrl/⌘-click opens the disease page) · drag a node to pin it in place · scroll/pinch to zoom.

Member diseases (most connected first ‐ the cluster's core)

Disease ⇵ Connections in cluster ⇵ Significant partners ⇵ Curated genes ⇵
Microcephaly 9 9 159
Primary microcephaly 6 6 36
Autosomal recessive primary microcephaly 5 5 24
Congenital microcephaly 5 5 31
Seckel syndrome 4 4 18
Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities 2 2 1
Cerebellofaciodental syndrome 1 1 1
Diffuse cerebral and cerebellar atrophy–intractable seizures–progressive microcephaly syndrome 1 1 1
Ehlers-danlos syndrome, hypermobility type 1 1 1
Microcephaly, congenital cataract, and psoriasiform dermatitis 1 1 1
Microcephaly, postnatal progressive, with seizures and brain atrophy 1 1 1
Neurodevelopmental disorder with feeding difficulties, thin corpus callosum, and foot deformity 1 1 1
Neurodevelopmental disorder with microcephaly and movement abnormalities 1 1 1
Neurodevelopmental disorder with microcephaly, short stature, and speech delay 1 1 1
Seckel syndrome 10 1 1 1

Top shared genes (genes linked to 2+ member diseases)

Gene ⇵ Member diseases ⇵ Linked diseases
CDK5RAP2 5 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly and 1 more
CEP152 5 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly and 1 more
CPAP 5 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly and 1 more
ASPM 4 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly
CENPE 4 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly, Seckel syndrome
CIT 4 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly
KNL1 4 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly
MCPH1 4 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly
MFSD2A 4 / 15 Autosomal recessive primary microcephaly, Microcephaly, Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities, Primary microcephaly
PHC1 4 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly
STIL 4 / 15 Autosomal recessive primary microcephaly, Congenital microcephaly, Microcephaly, Primary microcephaly
ANKLE2 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
CDK6 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
CEP135 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
CEP63 3 / 15 Microcephaly, Primary microcephaly, Seckel syndrome
COPB2 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
KIF14 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
NCAPD3 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
NUP37 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
RNF17 3 / 15 Congenital microcephaly, Microcephaly, Seckel syndrome
SASS6 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
TRAPPC14 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
WDR62 3 / 15 Congenital microcephaly, Microcephaly, Primary microcephaly
ZNF335 3 / 15 Autosomal recessive primary microcephaly, Microcephaly, Primary microcephaly
ANGPT2 2 / 15 Microcephaly, Primary microcephaly
BRF1 2 / 15 Cerebellofaciodental syndrome, Congenital microcephaly
BUB1 2 / 15 Autosomal recessive primary microcephaly, Microcephaly
CASK 2 / 15 Congenital microcephaly, Microcephaly
DPP6 2 / 15 Microcephaly, Primary microcephaly
FOXG1 2 / 15 Congenital microcephaly, Microcephaly
LMNB1 2 / 15 Microcephaly, Primary microcephaly
MCM7 2 / 15 Microcephaly, Primary microcephaly
MED17 2 / 15 Microcephaly, Microcephaly, postnatal progressive, with seizures and brain atrophy
MSMO1 2 / 15 Microcephaly, Microcephaly, congenital cataract, and psoriasiform dermatitis
NCAPD2 2 / 15 Autosomal recessive primary microcephaly, Microcephaly
NCAPH 2 / 15 Autosomal recessive primary microcephaly, Microcephaly
NSMCE2 2 / 15 Seckel syndrome, Seckel syndrome 10
OLA1 2 / 15 Ehlers-danlos syndrome, hypermobility type, Microcephaly
PDCD6IP 2 / 15 Microcephaly, Primary microcephaly
PLK4 2 / 15 Microcephaly, Seckel syndrome
PNKP 2 / 15 Congenital microcephaly, Microcephaly
POC1A 2 / 15 Microcephaly, Primary microcephaly
QARS1 2 / 15 Diffuse cerebral and cerebellar atrophy–intractable seizures–progressive microcephaly syndrome, Microcephaly
RAB11A 2 / 15 Congenital microcephaly, Microcephaly
RBBP8 2 / 15 Microcephaly, Seckel syndrome
RTTN 2 / 15 Congenital microcephaly, Microcephaly
TAF2 2 / 15 Microcephaly, Neurodevelopmental disorder with feeding difficulties, thin corpus callosum, and foot deformity
TEDC1 2 / 15 Microcephaly, Primary microcephaly
TRAIP 2 / 15 Microcephaly, Seckel syndrome
TRAPPC10 2 / 15 Neurodevelopmental disorder with microcephaly, short stature, and speech delay, Primary microcephaly
TTI1 2 / 15 Microcephaly, Neurodevelopmental disorder with microcephaly and movement abnormalities
What do these columns mean?
Connections in cluster
How many other members this disease has a shared-gene link to (the node size in the network above). The most-connected diseases are the cluster's core.
Significant partners
How many of those links are statistically significant (FDR q < 0.05).
Curated genes
Distinct curated genes linked to that disease in GeDiPNet.
Member diseases (Top shared genes)
How many of this cluster's diseases are linked to the gene, out of the cluster's total. Genes shared by many members are the most direct explanation of why they group together.
Overlap genes (x / y)
x = genes shared between this cluster and the pathway/GO term; y = that pathway/GO term's total gene count. A higher x relative to y (and to the cluster's own size) means a tighter biological match.
Cluster gene count
Total distinct genes across every disease in this cluster -- the "n" used in the significance test below.
Fold enrichment
Observed overlap divided by the overlap expected by chance, given the cluster's gene count, the pathway/term's size and the gene universe tested. 5× means five times more shared genes than random. Tells strong hits apart when q-values are all vanishingly small.
P-value / FDR q-value
Is this pathway/GO term's overlap with the cluster more than chance? Upper-tail hypergeometric test, Benjamini-Hochberg corrected across every tested pathway/term (prefer the q-value -- it accounts for testing many at once).
Shared genes (Pairs within this cluster)
Number of curated genes the two diseases in that row have in common.
Similarity score (Pairs within this cluster)
Jaccard-based gene overlap between the two specific diseases in that row -- same metric as the main Shared-Gene Disease Pairs page.

Enriched Pathways (why this cluster is grouped, biologically)

Pathway ⇵ Source ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
Recruitment of NuMA to mitotic centrosomes
CDK5RAP2, CEP135, CEP152, CEP63, MZT2B, TUBA3E, DYNC1H1, PLK4, TUBA1A, TUBG1, TUBGCP4, TUBGCP6
 Reactome 16 / 94 10.8× 1.17e-12 2.20e-10 ✓ sig.
Recruitment of mitotic centrosome proteins and complexes
CDK5RAP2, CEP135, CEP152, CEP63, MZT2B, DYNC1H1, PLK4, TUBA1A, TUBG1, TUBGCP4, TUBGCP6, NDE1
 Reactome 15 / 82 11.6× 2.04e-12 3.61e-10 ✓ sig.
Loss of Nlp from mitotic centrosomes
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, NDE1, PPP2R1A, PCNT, PLK1
 Reactome 12 / 70 10.9× 7.80e-10 7.42e-8 ✓ sig.
Loss of proteins required for interphase microtubule organization from the centrosome
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, NDE1, PPP2R1A, PCNT, PLK1
 Reactome 12 / 70 10.9× 7.80e-10 7.42e-8 ✓ sig.
Resolution of Sister Chromatid Cohesion
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 15 / 126 7.6× 1.15e-9 1.05e-7 ✓ sig.
AURKA Activation by TPX2
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, NDE1, PPP2R1A, PCNT, PLK1
 Reactome 12 / 73 10.4× 1.29e-9 1.17e-7 ✓ sig.
Mitotic Prometaphase
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 14 / 113 7.9× 2.48e-9 2.11e-7 ✓ sig.
EML4 and NUDC in mitotic spindle formation
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 14 / 117 7.6× 3.93e-9 3.22e-7 ✓ sig.
Anchoring of the basal body to the plasma membrane
CDK5RAP2, CEP135, CEP152, CEP63, RAB11A, DYNC1H1, PLK4, TUBA1A, TUBG1, NDE1, PPP2R1A, PCNT
 Reactome 13 / 98 8.4× 4.01e-9 3.27e-7 ✓ sig.
RHO GTPases Activate Formins
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 15 / 140 6.8× 5.05e-9 4.01e-7 ✓ sig.
Regulation of PLK1 Activity at G2/M Transition
CDK5RAP2, CEP135, CEP152, CEP63, DYNC1H1, PLK4, TUBA1A, TUBG1, NDE1, PPP2R1A, PCNT, PLK1
 Reactome 12 / 88 8.7× 1.18e-8 8.56e-7 ✓ sig.
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
CENPE, KNL1, NUP37, BUB1B, DYNC1H1, KIF2A, SPDL1, BUB1, NDE1, PPP2R1A, NUP85, PLK1
 Reactome 12 / 96 7.9× 3.21e-8 2.08e-6 ✓ sig.
Separation of Sister Chromatids
CENPE, KNL1, NUP37, TUBA3E, BUB1B, DYNC1H1, KIF2A, SPDL1, TUBA1A, BUB1, NDE1, PPP2R1A
 Reactome 16 / 190 5.4× 4.94e-8 3.01e-6 ✓ sig.
HDR through Single Strand Annealing (SSA)
RBBP8, TOP3A, NBN, ATR, ATRIP, DNA2, KAT5
 Reactome 7 / 37 12.0× 1.48e-6 5.86e-5 ✓ sig.
Presynaptic phase of homologous DNA pairing and strand exchange
RBBP8, TOP3A, NBN, ATR, ATRIP, DNA2, KAT5
 Reactome 7 / 39 11.4× 2.15e-6 8.03e-5 ✓ sig.

Enriched GO Terms (Biological Process, a second line of biological evidence)

GO term ⇵ GO ID ⇵ Overlap genes ⇵ Fold enrichment ⇵ P-value ⇵ FDR q-value ⇵
cell division
ANKLE2, ASPM, CDK6, CENPE, CEP63, CIT, KIF14, KNL1, NCAPD3, NUP37, PDCD6IP, INO80
 GO:0051301 30 / 406 7.3× 1.24e-17 1.43e-14 ✓ sig.
centriole replication
CDK5RAP2, CEP135, CEP152, CEP63, SASS6, WDR62, RTTN, PLK4, CEP295
 GO:0007099 9 / 24 37.1× 1.05e-12 4.95e-10 ✓ sig.
cerebral cortex development
ASPM, KIF14, MCPH1, WDR62, FOXG1, NR2E1, SLC2A1, TUBA1A, NDE1, EOMES, WDR47, SMO
 GO:0021987 13 / 88 14.6× 4.74e-12 1.94e-9 ✓ sig.
mitotic spindle organization
CENPE, STIL, WDR62, DYNC1H1, KIF2A, TUBG1, KIF11, PCNT, POC1A, PLK1
 GO:0007052 10 / 58 17.0× 3.02e-10 8.22e-8 ✓ sig.
microtubule cytoskeleton organization
CDK5RAP2, TUBA3E, KIF2A, KIFBP, TBCD, TUBA1A, TUBG1, RHO, GAPDH, TUBGCP4, TUBGCP6, NUSAP1
 GO:0000226 14 / 149 9.3× 3.56e-10 9.51e-8 ✓ sig.
mitotic cell cycle
CENPE, CIT, MCPH1, TUBA3E, TBCD, TUBA1A, TUBG1, NCAPD2, TUBGCP4, TUBGCP6, KIF11, PLK1
 GO:0000278 12 / 142 8.4× 2.24e-8 3.55e-6 ✓ sig.
DNA damage response
CDK6, CEP63, MCM7, INO80, PNKP, SMARCAL1, CTLA4, ERCC6, TRAIP, TP53BP1, RBBP8, WDR4
 GO:0006974 22 / 577 3.8× 9.77e-8 1.24e-5 ✓ sig.
microtubule-based movement
CENPE, KIF14, DNAH2, RAB11A, DYNC1H1, KIF2A, KIF5C, KIF11, KIF21B
 GO:0007018 9 / 87 10.2× 2.38e-7 2.61e-5 ✓ sig.
double-strand break repair via nonhomologous end joining
PNKP, SMARCAL1, TP53BP1, NSMCE2, HMGB1, DYRK1A, KAT5
 GO:0006303 7 / 45 15.4× 3.18e-7 3.34e-5 ✓ sig.
positive regulation of neuroblast proliferation
ASPM, WDR62, ZNF335, FOXG1, NR2E1, SMO
 GO:0002052 6 / 29 20.5× 3.87e-7 3.92e-5 ✓ sig.
DNA damage checkpoint signaling
CEP63, DONSON, ERCC6, TP53BP1, NBN, ATR, ATRIP
 GO:0000077 7 / 47 14.7× 4.33e-7 4.31e-5 ✓ sig.
mitotic chromosome condensation
NCAPD3, NCAPD2, NCAPH, NUSAP1, PLK1
 GO:0007076 5 / 17 29.1× 5.63e-7 5.38e-5 ✓ sig.
tRNA-type intron splice site recognition and cleavage
TSEN2, TSEN34, TSEN54
 GO:0000379 3 / 3 98.9× 1.02e-6 8.72e-5 ✓ sig.
brain development
ASPM, CDK5RAP2, MFSD2A, ZNF335, AFF2, FOXG1, QARS1, NR2E1, EOMES, WDR47, UFC1, UFM1
 GO:0007420 13 / 244 5.3× 1.26e-6 1.04e-4 ✓ sig.
DNA repair
INO80, PNKP, SMARCAL1, ERCC6, TRAIP, TP53BP1, RBBP8, TOP3A, NBN, ATR, ATRIP, DNA2
 GO:0006281 17 / 420 4.0× 1.35e-6 1.10e-4 ✓ sig.

Pairs within this cluster, by significance

Disease A ⇵ Disease B ⇵ Similarity score ⇵ Shared genes ⇵ P-value ⇵ FDR q-value ⇵
Autosomal recessive primary microcephaly Primary microcephaly 0.525 21 5.96e-56 1.71e-54 ✓ sig.
Microcephaly Primary microcephaly 0.181 30 2.26e-55 6.43e-54 ✓ sig.
Autosomal recessive primary microcephaly Microcephaly 0.150 24 3.07e-49 8.18e-48 ✓ sig.
Congenital microcephaly Microcephaly 0.091 16 1.85e-24 3.11e-23 ✓ sig.
Congenital microcephaly Primary microcephaly 0.172 10 5.00e-20 7.33e-19 ✓ sig.
Autosomal recessive primary microcephaly Congenital microcephaly 0.191 9 1.83e-19 2.63e-18 ✓ sig.
Primary microcephaly Seckel syndrome 0.100 5 4.26e-10 3.80e-9 ✓ sig.
Autosomal recessive primary microcephaly Seckel syndrome 0.103 4 1.34e-8 1.05e-7 ✓ sig.
Congenital microcephaly Seckel syndrome 0.087 4 3.94e-8 2.92e-7 ✓ sig.
Seckel syndrome Seckel syndrome 10 0.053 1 1.16e-3 1.73e-3 ✓ sig.
Autosomal recessive primary microcephaly Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities 0.040 1 1.55e-3 2.19e-3 ✓ sig.
Cerebellofaciodental syndrome Congenital microcephaly 0.031 1 2.00e-3 2.72e-3 ✓ sig.
Neurodevelopmental disorder with microcephaly, short stature, and speech delay Primary microcephaly 0.027 1 2.32e-3 3.05e-3 ✓ sig.
Neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities Primary microcephaly 0.027 1 2.32e-3 3.05e-3 ✓ sig.
Diffuse cerebral and cerebellar atrophy–intractable seizures–progressive microcephaly syndrome Microcephaly 0.006 1 1.03e-2 1.14e-2 ✓ sig.
Ehlers-danlos syndrome, hypermobility type Microcephaly 0.006 1 1.03e-2 1.14e-2 ✓ sig.
Microcephaly Microcephaly, congenital cataract, and psoriasiform dermatitis 0.006 1 1.03e-2 1.14e-2 ✓ sig.
Microcephaly Microcephaly, postnatal progressive, with seizures and brain atrophy 0.006 1 1.03e-2 1.14e-2 ✓ sig.
Microcephaly Neurodevelopmental disorder with feeding difficulties, thin corpus callosum, and foot deformity 0.006 1 1.03e-2 1.14e-2 ✓ sig.
Microcephaly Neurodevelopmental disorder with microcephaly and movement abnormalities 0.006 1 1.03e-2 1.14e-2 ✓ sig.